Skepticism

EVENTS

Who needs an IQ test when you’ve got coalescence?

I am just blown away by the consistency of this observation. You know, the creationists are not all stupid; there’s a wide range of intelligence in their camp, even if they are all wrong. But this one recent paper on the gorilla genome has become such an excellent tool for discriminating the competent from the incompetent.

Until recently, the answer was that a real family tree should generate a fully consistent pattern of similarities. [Not true at all. Coalescent theory is an extension of Fisher/Wright models of large populations, and the formal mathematics were worked out in the 1980s] For example, we are told that chimps and humans came from the same ancestral stock (call it CH stock) and that gorillas, chimps and humans all came from an earlier ancestral stock (GCH stock) [Correct so far]. If so, then the human and chimp genomes should consistently be more similar to each other than either is to the gorilla genome [WRONG. They should not be consistently more similar. Does he know nothing of probability?], since the human and chimp histories were one and the same thing more recently than the human and gorilla (or chimp and gorilla) histories were.

Well, the recent publication of the gorilla genome sequence shows that the expected pattern just isn’t there [Jebus. Read the paper. The pattern observed is the expected pattern.]. Instead of a nested hierarchy of similarities, we see something more like a mosaic [AS WE’D EXPECT.]. According to a recent report, “In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other…”

That’s sufficiently difficult to square with Darwin’s tree that it ought to bring the whole theory into question. And in an ideal world where Darwinism is examined the way scientific theories ought to be examined, I think it would. But in the real world things aren’t always so simple [And yet the creationists keep throwing up their simplistic models and being surprised that they’re wrong].

Axe is the one guy the creationists keep touting as a real scientist, a guy with genuine chops in molecular biology, the man who is doing serious scientific work. You know, if you’re going to publicly criticize an observation and claim it calls into question the entirety of evolutionary theory, you ought to first look into it and see whether that observation actually fits a prediction of evolution — actual evolutionary theory, not that cartoonishly naive caricature of evolution the creationists all have in their heads.

Here’s a nice, short history of coalescent theory by Kingman. It’s been around for decades, long before the gorilla genome was sequenced, and it predicted what kinds of distributions we ought to see in our comparisons of different species…predictions that were borne out by the paper Axe thinks contradicts evolutionary theory.

You know, if I was going to write a public takedown of a major scientific theory, I would probably try to first run my complaints by someone who thought the theory was correct. I’d get a friend or correspondent with expertise in the area to tell me exactly where he or she thought I was wrong — and I’d pay special attention to this. I’d then correct anything on my part which seemed grossly incorrect, ignoring only what I thought stood up under criticism. But then, I’m cautious.

I suspect that Creationists, when they look for peer review, always look for peer review from their friends — other Creationists. If so, they ought to try doing it the other way. It could save embarrassment.

Unless, of course, they are only trying to write something that sounds convincing to the already convinced.

So all one has to do as an ID10T ‘scientist’ is look at a paper showing, once again, that evolution really does explain reality, pick one or two things out of context, and declare they mean the opposite?

Hmmm.

I wonder how much they pay? I’ve got two kids in college . . . . Toss an honorary PhD my direction and . . . .

Looking at pieces like this makes me think that if there was such a thing as The Final Proof for Evolution ™ and it was published then next day creationist website would have paper titled “Final Proof for Evolution ™ proves evolution wrong”…

What do they think of introgression? That is, when genes invade one population from another after they’ve been separated and have become distinct? Just a few genes increase in frequency, rather than all genes from the other population occurring at the same frequency. I think I remember from my university days a Bernatchez paper about Arctic char mitochondria invading a northern brook trout population (the Arctic char mitochondria were more efficient in colder water, and so were positively selected in this brook trout population). How would Axe respond to that?

BTW, I haven’t looked at the Gorilla paper. I believe the Fisher/Wright (particularly Wright) models mostly assumed selectively neutral alleles. Is there a distinction made between neutral and selected loci in the gorilla paper? Would it be useful/necessary to investigate these differences to get a clear picture of what happened in our past?

It seems this guy, and Creationists in general, suffer from an error in thinking that punching a hole in “Darwin” invalidates all of evolution and simultaneously validates creationism. This does not follow. These beliefs are as wrong headed as this guys conclusions from the gorillas genome research. But then, these are people who put stock in “belief” which is dangerously misguided.

@slatham: Yes selection is indeed an important and interesting aspect of this. The impact of selection at a locus is to decrease the effective population size there. This has the consequence of reducing the amount of incomplete lineage sorting (ILS) – e.g. at selected loci there is less chance of human finding a common ancestor with gorilla before chimp. As a result, we would expect to see less ILS near genes, and it turns out this is the case: whereas human is closer to gorilla at 15% of sites across the genome as a whole, this reduces to about 10% in sites close to genes.

In the gorilla genome paper we explored this variation as a way to investigate the impact of natural selection on the genome within the population ancestral to both humans and chimpanzees (Fig. 2b in the paper).

See, here’s the thing. They already know they’re right a priori. God said so. If coalescence theory contradicts their interpretation of this gorilla study, then there must be something wrong with it. Whatever contradicts what God told them will ultimately prove to be wrong because he’s all-powerful, and never would have told them he created man if he hadn’t. What reason does an omnipotent superhero have to lie to one of his lowly creations? You don’t see me telling lies to my lego mindstorm robot do you?

See how it works? Science that agrees with me is a useful tool. Science that disagrees with me can be safely ignored.

Surely it doesn’t matter if the analysis is wrong. The creationists are preaching to people who don’t want to believe evolution is true & don’t understand it. All they need to do is present a simple argument that “disproves” evolution & the faithful will be convinced. Their audience don’t need the science to be right, only to justify their already formed conclusions.

I had a look through your description of coalescence and it did seem a bit far fetched. If you have a mutation occurring before the HC speciation, Then you would expect both alleles to occur in chimps and humans, unless there were selective pressures specific to each species. To have this unlikely event account for 30% of the genome seems far fetched.

It seems far simpler to posit that the mutation occurred after the speciation event. Say it happened to a chimp, then spread through the chimp population. Now humans and gorillas have the “old” gene, and chimps have the “new” gene.

This seems much more likely to explain the phenomenon. Any reason why I could be wrong here?

Ramirofernandez: The explanation depends on incomplete lineage sorting…lineage sorting is the random extinction of alleles in populations due to drift. When this is incomplete, because population size is large enough to limit drift in some branches of the tree, the mosaic pattern is exactly what is predicted.

Also, it is more fun and magical to refer to coalescence theory as simply “The Coalescent”.

OK, I don’t know any biology but this bloke’s supposed to be a scientist in the field. If so, he must know the facts, so why is he spouting this crap? Is it deliberate obfuscation (as I suspect) or is he really just stupid?

“The rest of the oil in his palm the priest shall put on the head of the one to be cleansed, to make atonement for them before the LORD. 30 Then he shall sacrifice the doves or the young pigeons, such as the person can afford, 31 one as a sin offering and the other as a burnt offering, together with the grain offering. In this way the priest will make atonement before the LORD on behalf of the one to be cleansed.”

32 These are the regulations for anyone who has a defiling skin disease and who cannot afford the regular offerings for their cleansing.”

shaguhhoo #18 – I am sure they would have some explanation – some rationalization to show you just are misinterpreting the bible because you have not studied it like they have with the light of the Lord in the hearts and eyes.

And you know I agree with them on this: it takes SPECIAL POWERS to make Leviticus or most anything in the Babble or subsequent doctrine and dogma seem like something other than:

(1) the primitive ravings of the elite to maintain their high positions and to control scared ignorant people

(2) the ravings of people who recognized the need for some social and philosophical reforms and then those of others who seized the movement to leverage their political aims

As to subject matter of the post: Sastra #4 hit a nail on the head.

We know there is no conspiracy to maintain “the false T of E”. If legit research and scientific analysis and conclusions lead us from T of E to something better, truer, more useful, why we know (1) scientists be all ears and (2) who the next Nobel prize winners would be.

If Axe is a scientist he should know this and the methods and means for presenting and gaining acceptance of hypothesis and conclusions.

Since people like Axe do not do as they should do as “scientists” we have to conclude what we conclude: liar, lunatic, dolt, charlatan, or all or any of above.

I’m not well up in Biology, but I think I get the whole coalescence thing. I think this is the heart of the idea :” Thus, the genes of one generation are represented by N points on the line. As we observe from generation to generation, the N points perform a “coherent random walk.” The group strays farther and farther from its starting point, but the extent of the group remains relatively limited, and the distribution of the relative positions of the points converges to a proper limit. ”
(Kingman, Origins of the Coalescent: 1974–1982 )
I’m not sure how this is supposed to be “a danger to evolution”, as it only seems to specify a mechanism of evolutionary change and not to re-define evolution itself. Of course, some genes in different but closely related species are to be expected. Why should there not be ? Seems to me Axe is being a bit dull about the whole thing. (pun intended.)

I sent the dear fellow an email congratulating him on his continual failure to understand the science, and suggesting his next headline should be something along the lines of, “Evolutionists use time travel to change theory, so that it says that new gorilla evidence doesn’t contradict it.”

After all, this is almost always, without the time travel part, their very next claim, that somehow scientists change the theory so it claims to predict what was just discovered. They just leave out the inconvenient detail that this tends to happen ***before*** they find the new evidence, you know, kind of like its a prediction, not a post hoc revision…